An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes

Jyotsna Talreja Wassan; Huiru Zheng; Browne Fiona; Jenna Bowen; Paul Walsh; Rainer Roehe; Richard Dewhurst; Cintia Palu; Brian Kelly; Haiying / HY Wang

doi:10.1109/BIBM.2018.8621104

An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes

Jyotsna Talreja Wassan, Huiru Zheng, Browne Fiona, Jenna Bowen, Paul Walsh, Rainer Roehe, Richard Dewhurst, Cintia Palu, Brian Kelly, Haiying / HY Wang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

5 Citations (Scopus)

157 Downloads (Pure)

Abstract

Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.

Original language	English
Title of host publication	Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018
Editors	Harald Schmidt, David Griol, Haiying Wang, Jan Baumbach, Huiru Zheng, Zoraida Callejas, Xiaohua Hu, Julie Dickerson, Le Zhang
Place of Publication	Madrid, Spain
Publisher	IEEE
Pages	1854-1860
Number of pages	7
ISBN (Electronic)	9781538654880
ISBN (Print)	978-1-5386-5489-7
DOIs	https://doi.org/10.1109/BIBM.2018.8621104
Publication status	Published (in print/issue) - 24 Jan 2019

Keywords

Phylogeny
Cows
Radio frequency
Predictive models
Vegetation
Pipelines
Tools
machine Learning
classification
metagenomics
ordination
Cattle Microbiomes
phylogeny

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10.1109/BIBM.2018.8621104

BIBM2018_S10203_acceptedVersionAuthor Accepted Manuscript, 355 KB

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Wassan, J. T., Zheng, H., Fiona, B., Bowen, J., Walsh, P., Roehe, R., Dewhurst, R., Palu, C., Kelly, B., & Wang, H. . HY. (2019). An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes. In H. Schmidt, D. Griol, H. Wang, J. Baumbach, H. Zheng, Z. Callejas, X. Hu, J. Dickerson, & L. Zhang (Eds.), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 (pp. 1854-1860). Article 8621104 IEEE. https://doi.org/10.1109/BIBM.2018.8621104

Wassan, Jyotsna Talreja ; Zheng, Huiru ; Fiona, Browne et al. / An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes. Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. editor / Harald Schmidt ; David Griol ; Haiying Wang ; Jan Baumbach ; Huiru Zheng ; Zoraida Callejas ; Xiaohua Hu ; Julie Dickerson ; Le Zhang. Madrid, Spain : IEEE, 2019. pp. 1854-1860

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abstract = "Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.",

keywords = "Phylogeny, Cows, Radio frequency, Predictive models, Vegetation, Pipelines, Tools, machine Learning, classification, metagenomics, ordination, Cattle Microbiomes, phylogeny",

author = "Wassan, {Jyotsna Talreja} and Huiru Zheng and Browne Fiona and Jenna Bowen and Paul Walsh and Rainer Roehe and Richard Dewhurst and Cintia Palu and Brian Kelly and Wang, {Haiying / HY}",

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doi = "10.1109/BIBM.2018.8621104",

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Wassan, JT, Zheng, H , Fiona, B, Bowen, J, Walsh, P, Roehe, R, Dewhurst, R, Palu, C, Kelly, B & Wang, HHY 2019, An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes. in H Schmidt, D Griol, H Wang, J Baumbach, H Zheng, Z Callejas, X Hu, J Dickerson & L Zhang (eds), Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018., 8621104, IEEE, Madrid, Spain, pp. 1854-1860. https://doi.org/10.1109/BIBM.2018.8621104

An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes. / Wassan, Jyotsna Talreja; Zheng, Huiru ; Fiona, Browne et al.
Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. ed. / Harald Schmidt; David Griol; Haiying Wang; Jan Baumbach; Huiru Zheng; Zoraida Callejas; Xiaohua Hu; Julie Dickerson; Le Zhang. Madrid, Spain: IEEE, 2019. p. 1854-1860 8621104.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes

AU - Wassan, Jyotsna Talreja

AU - Zheng, Huiru

AU - Fiona, Browne

AU - Bowen, Jenna

AU - Walsh, Paul

AU - Roehe, Rainer

AU - Dewhurst, Richard

AU - Palu, Cintia

AU - Kelly, Brian

AU - Wang, Haiying / HY

PY - 2019/1/24

Y1 - 2019/1/24

N2 - Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.

AB - Metagenomics is the study of environmental microbial communities and has various applications and implications in biological research. This paper aims to study the role of microbial communities in cattle rumen and their relation to probiotic diet supplement usage as part of the EU H2020 MetaPIat project l1 MetaPlat, http://www.metaplat.eu. In this research, we proposed and evaluated a computational framework to classify 16S rRNA samples from Bos taurus (cattle) rumen microbiome into a diet phenotype. We performed analysis by benchmarking various phylogeny-driven methods based on integration of biological domain knowledge of relationships and non-phylogenetic methods based on the raw abundances. The integrative approach incorporating phylogenetic tree structure into machine learning (ML) modelling achieved a high predictive performance with Accuracy of 0.925 and Kappa of 0.900 for classifying cattle microbiomes into diets supplemented with oil, nitrate, a combination and controls.

KW - Phylogeny

KW - Cows

KW - Radio frequency

KW - Predictive models

KW - Vegetation

KW - Pipelines

KW - Tools

KW - machine Learning

KW - classification

KW - metagenomics

KW - ordination

KW - Cattle Microbiomes

KW - phylogeny

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DO - 10.1109/BIBM.2018.8621104

M3 - Conference contribution

SN - 978-1-5386-5489-7

SP - 1854

EP - 1860

BT - Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018

A2 - Schmidt, Harald

A2 - Griol, David

A2 - Wang, Haiying

A2 - Baumbach, Jan

A2 - Zheng, Huiru

A2 - Callejas, Zoraida

A2 - Hu, Xiaohua

A2 - Dickerson, Julie

A2 - Zhang, Le

PB - IEEE

CY - Madrid, Spain

ER -

Wassan JT, Zheng H , Fiona B, Bowen J, Walsh P, Roehe R et al. An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes. In Schmidt H, Griol D, Wang H, Baumbach J, Zheng H, Callejas Z, Hu X, Dickerson J, Zhang L, editors, Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018. Madrid, Spain: IEEE. 2019. p. 1854-1860. 8621104 doi: 10.1109/BIBM.2018.8621104

An Integrative Framework for Functional Analysis of Cattle Rumen Microbiomes

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